It depends on how your flash object is put onto the page (post your code if you haven't resolved it) but usually you can fix this problem by setting the wmode parameter to transparent. Here is a link to the object/embed tag information from Adobe.
Add the following to your object tags:
<param name="wmode" value="transparent">
If you use something like swfobject to load your flash, you can set the wmode value in the javascript that loads the swf. Here's a rough example using there documentation:
var flashvars = {};
var params = {
wmode: "transparent"
};
var attributes = {};
swfobject.embedSWF("myContent.swf", "myContent", "300", "120", "9.0.0","expressInstall.swf", flashvars, params, attributes);